Abstract:Objective To compare the diagnostic accuracy of endoscopic ultrasound‑guided fine‑needle aspiration (FNA) and fine‑needle biopsy (FNB) for subepithelial lesions of the digestive system. Methods A retrospective study was conducted on patients with subcutaneous lesions of the digestive tract who were admitted to Beijing Friendship Hospital between January 2009 and December 2024. FNA and FNB were performed on subcutaneous space‑occupying lesions of the digestive tract that were confirmed by imaging examination. Logistic regression analysis was employed to identify factors associated with adequate immunohistochemical sampling. The diagnostic performance of FNA and FNB for gastrointestinal subepithelial lesions was evaluated using receiver operating characteristic curves, sensitivity, specificity, and accuracy. Results Among 145 patients, 56 underwent FNA and 89 underwent FNB. The FNB group showed a significantly higher immunohistochemical [87.64% (78/89) VS 67.86% (38/56), χ2=7.467, P=0.006] and pathological diagnostic success rate [93.26% (83/89) VS 82.14% (46/56), χ2=4.326, P=0.038] compared with the FNA group. The detection rate of stromal tumors in the FNB group was significantly higher than that in the FNA group [50.56% (45/89) VS 32.14% (18/56), χ2=5.143, P=0.023]. Logistic regression analysis results showed that FNB was a factor influencing the immunohistochemical success (P=0.012, OR=2.518, 95%CI: 1.262-6.319). However, tumor size <2 cm was an independent risk factor (P=0.048, OR=0.312, 95%CI: 0.082-0.933) for the failure of immunohistochemistry. Diagnostic sensitivity [93.98% (78/83) VS 78.26% (36/46)], specificity [100.00% (6/6) VS 80.00% (8/10)], and accuracy [94.38% (84/89) VS 78.57% (44/56)] of FNB were superior to FNA. The area under the curve for FNA and FNB in diagnosing subcutaneous space‑occupying lesions in the digestive tract were 0.791 (95%CI: 0.647-0.935) and 0.970 (95%CI: 0.944-0.996), respectively (P=0.020). Conclusion FNB exhibits distinct advantage over FNA in identifying subcutaneous space‑occupying lesions, particularly stromal tumor, within the digestive system. Therefore, FNB may be the preferred method for diagnosing such lesions.